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- PDB-3twx: Crystal structure of ARC4 from human Tankyrase 2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3twx
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human FNBP1 (chimeric peptide)
Components
  • Tankyrase-2
  • human FNBP1
KeywordsSIGNALING PROTEIN/PEPTIDE / ankyrin repeat / protein-protein interaction / substrate recruitment / poly(ADP-ribosyl)ation / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...: / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuettler, S. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis and sequence rules for substrate recognition by tankyrase explain the basis for cherubism disease.
Authors: Guettler, S. / Larose, J. / Petsalaki, E. / Gish, G. / Scotter, A. / Pawson, T. / Rottapel, R. / Sicheri, F.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: human FNBP1
D: human FNBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30112
Polymers39,4144
Non-polymers8878
Water2,972165
1
A: Tankyrase-2
C: human FNBP1
hetero molecules

B: Tankyrase-2
D: human FNBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30112
Polymers39,4144
Non-polymers8878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area6160 Å2
ΔGint-62 kcal/mol
Surface area15210 Å2
MethodPISA
2
A: Tankyrase-2
C: human FNBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2106
Polymers19,7072
Non-polymers5034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Tankyrase-2
D: human FNBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0916
Polymers19,7072
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.196, 74.176, 103.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Tankyrase-2 / TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose ...TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 17851.180 Da / Num. of mol.: 2 / Fragment: UNP residues 488-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide human FNBP1


Mass: 1856.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 173 molecules

#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M NaOAc pH 5.5, 2% (v/v) PEG 400, 2.5 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2010
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 31795 / Num. obs: 31795 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.3 / Redundancy: 7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.3 / % possible all: 89.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.638 Å / SU ML: 0.47 / σ(F): 0.29 / Phase error: 21.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 1598 5.05 %Random
Rwork0.1977 ---
obs0.1995 31622 98.24 %-
all-31622 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.155 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4323 Å2-0 Å2-0 Å2
2--0.111 Å20 Å2
3----0.5433 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 42 165 2829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072707
X-RAY DIFFRACTIONf_angle_d0.983654
X-RAY DIFFRACTIONf_dihedral_angle_d12.7231001
X-RAY DIFFRACTIONf_chiral_restr0.067401
X-RAY DIFFRACTIONf_plane_restr0.005480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85980.31131320.28422401X-RAY DIFFRACTION88
1.8598-1.92620.2621290.25212738X-RAY DIFFRACTION99
1.9262-2.00330.27051550.20892709X-RAY DIFFRACTION99
2.0033-2.09450.22971340.18812725X-RAY DIFFRACTION99
2.0945-2.20490.23021410.18942740X-RAY DIFFRACTION99
2.2049-2.3430.20621490.18292730X-RAY DIFFRACTION100
2.343-2.52390.24331470.18292723X-RAY DIFFRACTION99
2.5239-2.77780.20741490.18852789X-RAY DIFFRACTION100
2.7778-3.17950.2361240.19172805X-RAY DIFFRACTION100
3.1795-4.0050.22211590.1872804X-RAY DIFFRACTION99
4.005-35.64540.23521790.20782860X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.3396-0.9196-2.29176.71572.93584.03980.05520.1105-0.7947-0.0936-0.1508-0.05621.11990.1136-0.00470.36350.0803-0.02930.16170.00590.2113-7.2567-13.395-51.8384
27.8156-0.9428-5.29877.2166-0.32893.8739-0.1687-0.7588-0.04790.36120.0267-1.09590.36481.31060.10090.18570.0625-0.02950.31820.02660.2652-0.5162-5.0245-46.6792
33.6581-1.9068-2.39112.54741.27153.3902-0.06740.2754-0.1141-0.0230.06610.15530.53310.0921-0.00370.18690.0138-0.03140.1353-0.00760.1213-12.1103-6.5099-53.3293
47.9758-0.2609-4.96972.0961-1.76097.84340.1126-0.48820.82730.36350.0196-0.3134-0.51090.695-0.14360.1472-0.0165-0.04790.1649-0.02670.1904-6.07333.3527-48.9044
53.8977-1.1661-0.14461.89541.16634.3633-0.03880.2289-0.0686-0.0199-0.0080.08880.1351-0.3470.03950.0994-0.0181-0.0040.0780.0040.1067-19.9403-0.4472-52.9358
64.9810.4543-1.01561.154-0.3845.8670.0466-0.15710.95740.27070.01240.0357-0.96970.2243-0.10160.2056-0.0176-0.02030.099-0.02230.2006-15.88779.2708-46.5058
76.99623.41630.11585.78140.57462.5686-0.08030.63480.4375-0.2297-0.13420.2709-0.1364-0.36790.20380.09770.0478-0.00710.26640.01530.1417-26.01672.9873-56.8094
86.2507-0.21761.88863.4107-1.81267.0884-0.1922-0.72190.26080.2760.0784-0.17590.3571-0.41010.09960.15990.0195-0.0160.2672-0.03210.1567-29.9152.9068-46.3182
93.9586-1.5114-0.73432.11970.4572.0088-0.0879-0.39041.01140.15020.1447-0.4185-0.30660.0246-0.02380.17890.0758-0.09330.2007-0.17110.5313-26.103912.5389-45.0971
106.91621.5702-0.7375.15390.11624.0027-0.26140.83410.5636-0.4731-0.09330.071-0.1383-0.67240.23180.15980.0468-0.04540.359-0.01710.2469-36.05195.4255-55.4745
110.7051-1.25590.04894.1642.55953.642-0.3595-0.96270.55880.47220.22040.1077-0.1365-0.46530.12060.15910.1142-0.04040.5309-0.18680.3441-38.01117.8413-42.2007
125.48331.80894.81983.9490.34675.78070.068-0.08940.16550.0124-0.0573-0.7812-0.13591.1955-0.02320.17570.02630.02060.4225-0.02510.29643.47422.9374-21.6028
134.757-0.30150.15496.9126-1.46655.54780.26030.7436-0.5145-0.7235-0.0929-0.30250.76410.6349-0.0810.30130.1523-0.02230.406-0.05220.1978-0.7451-6.4623-27.5993
143.5699-0.44331.99880.2905-1.47147.83290.1967-0.0271-0.1350.4024-0.11620.09280.20170.2922-0.15310.27190.0236-0.00680.2159-0.02650.1394-3.0834-1.0785-15.7591
154.3397-0.51051.0715.55740.01685.5297-0.04680.00190.17960.11560.0482-0.267-0.3680.72570.00610.1549-0.03210.01520.12920.00940.1235-6.08447.0673-23.2601
162.79-1.2244-0.4076.0157-2.27226.18470.19610.1718-0.5917-0.1057-0.06340.23681.02580.249-0.1470.25690.0481-0.0340.1492-0.02990.1632-10.6772-5.6913-25.1371
172.5064-1.06710.45963.07551.14943.1417-0.0866-0.14170.12890.27230.0231-0.0414-0.30670.1280.0580.1784-0.0036-0.00180.065-0.0030.1065-13.99268.3205-20.7438
182.2509-2.9966-1.00345.5424-1.77078.1346-0.05770.0522-0.3581-0.2056-0.07470.59830.7719-0.52290.08130.1892-0.0322-0.01280.12710.00180.1275-20.69770.562-27.4138
193.33091.43160.68936.57720.57221.737-0.069-0.23310.13150.48440.02540.23360.0027-0.15190.04340.26880.04340.01070.1026-0.00610.1529-19.789211.9898-16.8191
203.5728-1.671-2.86186.60221.05297.37870.32880.23130.1734-0.7711-0.2363-0.2244-0.10180.1926-0.09280.33620.0927-0.03060.1467-0.03380.2126-21.404116.0469-27.1027
210.54020.0563-0.23152.0983-0.40690.48110.06490.1444-0.35910.2055-0.08980.5478-0.1567-0.1952-0.07760.24010.1041-0.08170.1642-0.10770.439-27.232214.4278-23.0553
220.5763-0.8601-0.09051.29290.06110.66860.26340.3995-0.3031-0.674-0.29360.615-0.0871-0.18480.17780.48890.2339-0.12760.2689-0.10110.3148-29.305321.2245-30.7435
236.5462-1.06492.40861.434-1.70684.26110.3183-0.0178-0.30390.1872-0.33920.26840.6072-0.6251-0.01740.211-0.04770.04270.1452-0.04710.153-23.0755-6.7516-44.389
244.0025-3.5054-1.86386.07270.5492.9041-0.0874-0.10140.3956-0.12190.3973-0.2194-0.62330.556-0.29930.2601-0.1073-0.01950.18620.0210.1518-9.600914.3218-29.1562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 487:502)
2X-RAY DIFFRACTION2chain 'A' and (resseq 503:511)
3X-RAY DIFFRACTION3chain 'A' and (resseq 512:538)
4X-RAY DIFFRACTION4chain 'A' and (resseq 539:548)
5X-RAY DIFFRACTION5chain 'A' and (resseq 549:571)
6X-RAY DIFFRACTION6chain 'A' and (resseq 572:580)
7X-RAY DIFFRACTION7chain 'A' and (resseq 581:594)
8X-RAY DIFFRACTION8chain 'A' and (resseq 595:604)
9X-RAY DIFFRACTION9chain 'A' and (resseq 605:614)
10X-RAY DIFFRACTION10chain 'A' and (resseq 615:628)
11X-RAY DIFFRACTION11chain 'A' and (resseq 629:644)
12X-RAY DIFFRACTION12chain 'B' and (resseq 487:502)
13X-RAY DIFFRACTION13chain 'B' and (resseq 503:511)
14X-RAY DIFFRACTION14chain 'B' and (resseq 512:521)
15X-RAY DIFFRACTION15chain 'B' and (resseq 522:538)
16X-RAY DIFFRACTION16chain 'B' and (resseq 539:548)
17X-RAY DIFFRACTION17chain 'B' and (resseq 549:571)
18X-RAY DIFFRACTION18chain 'B' and (resseq 572:580)
19X-RAY DIFFRACTION19chain 'B' and (resseq 581:594)
20X-RAY DIFFRACTION20chain 'B' and (resseq 595:604)
21X-RAY DIFFRACTION21chain 'B' and (resseq 605:627)
22X-RAY DIFFRACTION22chain 'B' and (resseq 628:644)
23X-RAY DIFFRACTION23chain 'C'
24X-RAY DIFFRACTION24chain 'D'

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